Substantial quantities solid waste from livestock are potential sources of nutrients for agroecological production on small-scale farms. The processes used to extract these wastes, however, must be capable of eliminating pathogenic microorganisms. We aimed to evaluate composting and vermicomposting processes by inoculating efficient microorganisms at the field scale. We used cattle and sheep manure with the inoculation of efficient microorganisms (EMs) at concentrations of 0, 2, and 4 mL L-1. In vermicomposting experiments, we added Lumbricus rubellus. After the maturation and stabilization phases of the compounds, concentrations of macronutrients, micronutrients, heavy metals, thermotolerant coliforms and Salmonella spp. were measured. We found that composting processes allowed high availability of macronutrients. Vermicomposting, associated with inoculation with 2 mL L-1 EMs, promoted the lowest concentration of thermotolerant coliforms, ensuring greater elimination of pathogens. The compost produced allowed the valuation of waste and use it as a quality organic fertilizer for agroecological production.